protected ColumnSelection colSel = new ColumnSelection();
- public boolean autoCalculateConsensus = true;
+ protected boolean autoCalculateConsensusAndConservation = true;
+
+ public boolean getAutoCalculateConsensusAndConservation()
+ { // BH 2019.07.24
+ return autoCalculateConsensusAndConservation;
+ }
+
+ public void setAutoCalculateConsensusAndConservation(boolean b)
+ {
+ autoCalculateConsensusAndConservation = b;
+ }
protected boolean autoCalculateStrucConsensus = true;
+ public boolean getAutoCalculateStrucConsensus()
+ { // BH 2019.07.24
+ return autoCalculateStrucConsensus;
+ }
+
+ public void setAutoCalculateStrucConsensus(boolean b)
+ {
+ autoCalculateStrucConsensus = b;
+ }
+
protected boolean ignoreGapsInConsensusCalculation = false;
protected ResidueShaderI residueShading = new ResidueShader();
// see note in mantis : issue number 8585
if (alignment.isNucleotide()
|| (conservation == null && quality == null)
- || !autoCalculateConsensus)
+ || !autoCalculateConsensusAndConservation)
{
return;
}
public void updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if (consensus == null || !autoCalculateConsensus)
+ if (consensus == null || !autoCalculateConsensusAndConservation)
{
return;
}
{
alignment.padGaps();
}
- if (autoCalculateConsensus)
+ if (autoCalculateConsensusAndConservation)
{
updateConsensus(ap);
}
- if (hconsensus != null && autoCalculateConsensus)
+ if (hconsensus != null && autoCalculateConsensusAndConservation)
{
updateConservation(ap);
}
public void clearSequenceColours()
{
sequenceColours.clear();
- };
+ }
@Override
public AlignViewportI getCodingComplement()